The intonation on the 6th isn't quite right (based on fretted @ 12fret. Harmonic is better) and there isn't really anything left to get out of it, so I probably screwed my measurements up slightly.
You may not have necessarily stuffed your measurements, sometimes the low E can just be tricky.

If you need to move the E6 saddle further away from the neck (intonation is sharp) you can remove the spring from the adjustment screw. That can allow at least a couple of mil more movement back. Sometimes just cutting down the spring length can be enough to get the intonation correct.

You don't really need the spring on there when the saddle is under a tensioned string. It mainly keeps the saddle in place when you take the strings off.